[Chimera-users] a question relate to Chimera

Dougherty, Matthew T matthewd at bcm.edu
Thu Aug 27 12:48:04 PDT 2015


I find using the tools>high order structure>Icosahedron to be a better approach for viruses, particularly when adjusting the sphere factor, and the orientation.  From that you can quickly determine the min/max radius of the capsid, and the curvature.

Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
===========================================================================
________________________________________
From: chimera-users-bounces at cgl.ucsf.edu <chimera-users-bounces at cgl.ucsf.edu> on behalf of Tom Goddard <goddard at sonic.net>
Sent: Thursday, August 27, 2015 1:51 PM
To: Chimera_mailing_list
Subject: Re: [Chimera-users] a question relate to Chimera

Hi Smith,

  You can approximately measure the radius of a virus map using the Chimera scale bar,  menu Tools / Higher-Order Structure / Scalebar.  Just show the scale bar and move it so it is centered on your virus and adjust its size manually until it matches the virus diameter.  It is crude.

  But if you want fill ratio in 3 dimensions why not just compute the volume of the box and the volume enclosed in the map at a reasonable contour level (menu Tools / Volume Data / Measure Volume and Area) then divide those two volumes.  If you need it as a one-dimensional fill ratio, not 3 dimensional then take the cube root of that.

        Tom


> On Aug 27, 2015, at 9:50 AM, Elaine Meng  wrote:
>
> On Aug 26, 2015, at 6:27 PM, Smith Liu  wrote:
>
>> Dear Elaine,
>> Thanks for the reply.
>>
>> Here let us consider the first question on "a particle has a diameter of 100 pixels ", which I think may be done by Chimera with your help. From http://www.imagescience.de/fsc/index.htm, we can download a software which can be used to calculate the resolution of the map by FSC. When we use that software for calculation, we need to input "Filling degree" D/L, where the value of object size D in voxels, and the L, the linear ssize of the 3D volume (x, y,z). A typical value of "Filling degree" D/L would be 0.66, indicating that 2/3 of the linear width of the 3D volume is filled by the object.
>>
>> Thus will you please show me by Chimera how can we know "the value of object size D in voxels"?
>>
>> I am looking forward to getting your reply.
>>
>> Best regards.
>> Smith
>
> Dear Smith,
> Please send Chimera questions to chimera-users at cgl.ucsf.edu (instead of to me directly).   Others may be able to answer your questions better than I can, for example in this case where I don’t know the answer.
>
> For linear size of the whole volume (the map), we already discussed that you can see the number of grid units (voxels) in X,Y,Z to the right of the dataset name in the Volume Viewer dialog, and see angstroms per grid unit in the Features: Coordinates section of Volume Viewer.  You could multiply the values to get the size of the map in angstroms.
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011437.html>
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011433.html>
>
> However, I don’t know how you could measure the voxel size of the object in Chimera.  As far as I know you could only estimate it by eye, or by measuring angstrom dimensions, converting to grid units, and then multiplying them to roughly estimate the area of the object in voxels.  It would only be an estimate, assuming your object is not a perfect circle or square.  See previous posts on measuring angstrom dimensions in a map:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010609.html>
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009503.html>
>
> My guess is that people would normally get this information from the software used in the original data collection, not by doing measurements in Chimera.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>


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